HEADER TRANSFERASE 16-SEP-15 5DRT
TITLE CRYSTAL STRUCTURE OF DOT1L IN COMPLEX WITH INHIBITOR CPD2 [2-(2-(5-
TITLE 2 ((2-CHLOROPHENOXY)METHYL)-1H-TETRAZOL-1-YL)ACETYL)-N-(4-
TITLE 3 CHLOROPHENYL)HYDRAZINECARBOXAMIDE]
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: UNP RESIDUES 2-333;
COMPND 5 SYNONYM: DOT1-LIKE PROTEIN,HISTONE H3-K79 METHYLTRANSFERASE,H3-K79-
COMPND 6 HMTASE,LYSINE N-METHYLTRANSFERASE 4;
COMPND 7 EC: 2.1.1.43;
COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 GENE: DOT1L, KIAA1814, KMT4;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS INHIBITOR, COMPLEX, METHYLTRANSFERASE, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR C.SCHEUFLER,C.GAUL,C.BE,H.MOEBITZ
REVDAT 3 10-JAN-24 5DRT 1 REMARK
REVDAT 2 07-SEP-16 5DRT 1 JRNL
REVDAT 1 15-JUN-16 5DRT 0
JRNL AUTH C.CHEN,H.ZHU,F.STAUFFER,G.CARAVATTI,S.VOLLMER,R.MACHAUER,
JRNL AUTH 2 P.HOLZER,H.MOBITZ,C.SCHEUFLER,M.KLUMPP,R.TIEDT,K.S.BEYER,
JRNL AUTH 3 K.CALKINS,D.GUTHY,M.KIFFE,J.ZHANG,C.GAUL
JRNL TITL DISCOVERY OF NOVEL DOT1L INHIBITORS THROUGH A
JRNL TITL 2 STRUCTURE-BASED FRAGMENTATION APPROACH.
JRNL REF ACS MED.CHEM.LETT. V. 7 735 2016
JRNL REFN ISSN 1948-5875
JRNL PMID 27563395
JRNL DOI 10.1021/ACSMEDCHEMLETT.6B00167
REMARK 2
REMARK 2 RESOLUTION. 2.69 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : BUSTER 2.11.5
REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER,
REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN,
REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.69
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.82
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 NUMBER OF REFLECTIONS : 29583
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING + TEST SET) : 0.176
REMARK 3 R VALUE (WORKING SET) : 0.175
REMARK 3 FREE R VALUE : 0.197
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT : 1480
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 15
REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.69
REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.78
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.99
REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2880
REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2128
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2736
REMARK 3 BIN R VALUE (WORKING SET) : 0.2095
REMARK 3 BIN FREE R VALUE : 0.2781
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 144
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 4984
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 59
REMARK 3 SOLVENT ATOMS : 177
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 67.17
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.97
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 9.72840
REMARK 3 B22 (A**2) : 9.72840
REMARK 3 B33 (A**2) : -19.45670
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.344
REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.354
REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.217
REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.364
REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.222
REMARK 3
REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797
REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912
REMARK 3
REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15
REMARK 3 TERM COUNT WEIGHT FUNCTION.
REMARK 3 BOND LENGTHS : 5171 ; 2.000 ; HARMONIC
REMARK 3 BOND ANGLES : 7022 ; 2.000 ; HARMONIC
REMARK 3 TORSION ANGLES : 1739 ; 2.000 ; SINUSOIDAL
REMARK 3 TRIGONAL CARBON PLANES : 122 ; 2.000 ; HARMONIC
REMARK 3 GENERAL PLANES : 747 ; 5.000 ; HARMONIC
REMARK 3 ISOTROPIC THERMAL FACTORS : 5171 ; 20.000 ; HARMONIC
REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC
REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL
REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL
REMARK 3 CHIRAL IMPROPER TORSION : 663 ; 5.000 ; SEMIHARMONIC
REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL
REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL
REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL
REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL
REMARK 3 IDEAL-DIST CONTACT TERM : 5614 ; 4.000 ; SEMIHARMONIC
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.010
REMARK 3 BOND ANGLES (DEGREES) : 1.06
REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.88
REMARK 3 OTHER TORSION ANGLES (DEGREES) : 19.08
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 2
REMARK 3
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: { A|* L|* }
REMARK 3 ORIGIN FOR THE GROUP (A): -44.1646 8.1727 9.0374
REMARK 3 T TENSOR
REMARK 3 T11: -0.1852 T22: -0.1212
REMARK 3 T33: -0.0977 T12: -0.0051
REMARK 3 T13: 0.0692 T23: -0.0018
REMARK 3 L TENSOR
REMARK 3 L11: 4.0574 L22: 2.8393
REMARK 3 L33: 0.6450 L12: -1.9095
REMARK 3 L13: -0.3100 L23: 0.1446
REMARK 3 S TENSOR
REMARK 3 S11: -0.0661 S12: -0.3613 S13: 0.1491
REMARK 3 S21: 0.3204 S22: 0.1131 S23: 0.5459
REMARK 3 S31: 0.0939 S32: -0.0881 S33: -0.0470
REMARK 3
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: { B|* M|* }
REMARK 3 ORIGIN FOR THE GROUP (A): -35.4927 37.4501 8.8796
REMARK 3 T TENSOR
REMARK 3 T11: -0.1486 T22: -0.1548
REMARK 3 T33: -0.0824 T12: 0.0328
REMARK 3 T13: 0.0271 T23: -0.0472
REMARK 3 L TENSOR
REMARK 3 L11: 3.6633 L22: 2.6266
REMARK 3 L33: 0.5275 L12: -1.3168
REMARK 3 L13: 0.7732 L23: -0.2541
REMARK 3 S TENSOR
REMARK 3 S11: 0.0410 S12: -0.1170 S13: 0.3833
REMARK 3 S21: 0.0439 S22: -0.0808 S23: 0.4435
REMARK 3 S31: -0.1761 S32: -0.0566 S33: 0.0398
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 5DRT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-SEP-15.
REMARK 100 THE DEPOSITION ID IS D_1000213705.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 26-JAN-12
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SLS
REMARK 200 BEAMLINE : X10SA
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.99986
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XSCALE
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29583
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.690
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 10.30
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.12500
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.5300
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.76
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 10.60
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.980
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: 1NW3
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 64.67
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.48
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3M K/NA TARTRATE 0.1M HEPES PH7.2,
REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z
REMARK 290 3555 -X+Y,-X,Z
REMARK 290 4555 -X,-Y,Z+1/2
REMARK 290 5555 Y,-X+Y,Z+1/2
REMARK 290 6555 X-Y,X,Z+1/2
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.82250
REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 36.82250
REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 36.82250
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLY A 0
REMARK 465 PRO A 1
REMARK 465 GLY A 2
REMARK 465 GLU A 3
REMARK 465 LYS A 4
REMARK 465 THR A 92
REMARK 465 THR A 93
REMARK 465 GLN A 94
REMARK 465 PRO A 95
REMARK 465 MET A 96
REMARK 465 LYS A 97
REMARK 465 LEU A 98
REMARK 465 ASN A 126
REMARK 465 ASN A 127
REMARK 465 TYR A 128
REMARK 465 GLU A 129
REMARK 465 PRO A 130
REMARK 465 SER A 302
REMARK 465 VAL A 303
REMARK 465 GLY A 333
REMARK 465 GLY B 0
REMARK 465 PRO B 1
REMARK 465 GLY B 2
REMARK 465 GLU B 3
REMARK 465 THR B 93
REMARK 465 GLN B 94
REMARK 465 PRO B 95
REMARK 465 MET B 96
REMARK 465 LYS B 97
REMARK 465 LEU B 98
REMARK 465 ASN B 126
REMARK 465 ASN B 127
REMARK 465 TYR B 128
REMARK 465 GLU B 129
REMARK 465 PRO B 130
REMARK 465 GLY B 301
REMARK 465 SER B 302
REMARK 465 VAL B 303
REMARK 465 PRO B 332
REMARK 465 GLY B 333
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 LYS A 29 CG CD CE NZ
REMARK 470 GLU A 56 CG CD OE1 OE2
REMARK 470 ASN A 57 CG OD1 ND2
REMARK 470 LYS A 66 CE NZ
REMARK 470 GLU A 69 CG CD OE1 OE2
REMARK 470 ARG A 73 CD NE CZ NH1 NH2
REMARK 470 LYS A 77 CG CD CE NZ
REMARK 470 ARG A 80 CD NE CZ NH1 NH2
REMARK 470 ASN A 99 CG OD1 ND2
REMARK 470 THR A 120 OG1 CG2
REMARK 470 ASP A 121 CG OD1 OD2
REMARK 470 GLU A 123 CG CD OE1 OE2
REMARK 470 LYS A 124 CG CD CE NZ
REMARK 470 LEU A 125 CG CD1 CD2
REMARK 470 PHE A 131 CG CD1 CD2 CE1 CE2 CZ
REMARK 470 GLU A 138 CG CD OE1 OE2
REMARK 470 LYS A 193 CD CE NZ
REMARK 470 LYS A 207 CE NZ
REMARK 470 ARG A 278 CD NE CZ NH1 NH2
REMARK 470 LYS A 300 CG CD CE NZ
REMARK 470 SER A 304 OG
REMARK 470 LYS B 4 CE NZ
REMARK 470 LYS B 29 CG CD CE NZ
REMARK 470 THR B 92 OG1 CG2
REMARK 470 ASN B 99 CG OD1 ND2
REMARK 470 GLU B 123 CG CD OE1 OE2
REMARK 470 LYS B 124 CG CD CE NZ
REMARK 470 PHE B 131 CG CD1 CD2 CE1 CE2 CZ
REMARK 470 GLU B 138 CD OE1 OE2
REMARK 470 THR B 139 OG1 CG2
REMARK 470 LYS B 180 CD CE NZ
REMARK 470 LYS B 193 CD CE NZ
REMARK 470 LYS B 207 CD CE NZ
REMARK 470 GLU B 230 CD OE1 OE2
REMARK 470 GLU B 248 CD OE1 OE2
REMARK 470 LYS B 261 CD CE NZ
REMARK 470 ARG B 278 CG CD NE CZ NH1 NH2
REMARK 470 ARG B 282 CG CD NE CZ NH1 NH2
REMARK 470 LYS B 300 CD CE NZ
REMARK 470 SER B 304 OG
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 THR A 139 -61.12 -141.30
REMARK 500 ASP B 28 -169.65 -160.71
REMARK 500 THR B 139 -59.36 -140.78
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 K B1001 K
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 LYS B 52 O
REMARK 620 2 LEU B 53 O 74.4
REMARK 620 3 MET B 55 O 82.6 90.1
REMARK 620 4 ASN B 57 OD1 67.0 141.4 84.7
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 5EG A 401
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue K B 1001
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 5EG B 1002
DBREF 5DRT A 2 333 UNP Q8TEK3 DOT1L_HUMAN 2 333
DBREF 5DRT B 2 333 UNP Q8TEK3 DOT1L_HUMAN 2 333
SEQADV 5DRT GLY A 0 UNP Q8TEK3 EXPRESSION TAG
SEQADV 5DRT PRO A 1 UNP Q8TEK3 EXPRESSION TAG
SEQADV 5DRT GLY A 333 UNP Q8TEK3 LYS 333 CLONING ARTIFACT
SEQADV 5DRT GLY B 0 UNP Q8TEK3 EXPRESSION TAG
SEQADV 5DRT PRO B 1 UNP Q8TEK3 EXPRESSION TAG
SEQADV 5DRT GLY B 333 UNP Q8TEK3 LYS 333 CLONING ARTIFACT
SEQRES 1 A 334 GLY PRO GLY GLU LYS LEU GLU LEU ARG LEU LYS SER PRO
SEQRES 2 A 334 VAL GLY ALA GLU PRO ALA VAL TYR PRO TRP PRO LEU PRO
SEQRES 3 A 334 VAL TYR ASP LYS HIS HIS ASP ALA ALA HIS GLU ILE ILE
SEQRES 4 A 334 GLU THR ILE ARG TRP VAL CYS GLU GLU ILE PRO ASP LEU
SEQRES 5 A 334 LYS LEU ALA MET GLU ASN TYR VAL LEU ILE ASP TYR ASP
SEQRES 6 A 334 THR LYS SER PHE GLU SER MET GLN ARG LEU CYS ASP LYS
SEQRES 7 A 334 TYR ASN ARG ALA ILE ASP SER ILE HIS GLN LEU TRP LYS
SEQRES 8 A 334 GLY THR THR GLN PRO MET LYS LEU ASN THR ARG PRO SER
SEQRES 9 A 334 THR GLY LEU LEU ARG HIS ILE LEU GLN GLN VAL TYR ASN
SEQRES 10 A 334 HIS SER VAL THR ASP PRO GLU LYS LEU ASN ASN TYR GLU
SEQRES 11 A 334 PRO PHE SER PRO GLU VAL TYR GLY GLU THR SER PHE ASP
SEQRES 12 A 334 LEU VAL ALA GLN MET ILE ASP GLU ILE LYS MET THR ASP
SEQRES 13 A 334 ASP ASP LEU PHE VAL ASP LEU GLY SER GLY VAL GLY GLN
SEQRES 14 A 334 VAL VAL LEU GLN VAL ALA ALA ALA THR ASN CYS LYS HIS
SEQRES 15 A 334 HIS TYR GLY VAL GLU LYS ALA ASP ILE PRO ALA LYS TYR
SEQRES 16 A 334 ALA GLU THR MET ASP ARG GLU PHE ARG LYS TRP MET LYS
SEQRES 17 A 334 TRP TYR GLY LYS LYS HIS ALA GLU TYR THR LEU GLU ARG
SEQRES 18 A 334 GLY ASP PHE LEU SER GLU GLU TRP ARG GLU ARG ILE ALA
SEQRES 19 A 334 ASN THR SER VAL ILE PHE VAL ASN ASN PHE ALA PHE GLY
SEQRES 20 A 334 PRO GLU VAL ASP HIS GLN LEU LYS GLU ARG PHE ALA ASN
SEQRES 21 A 334 MET LYS GLU GLY GLY ARG ILE VAL SER SER LYS PRO PHE
SEQRES 22 A 334 ALA PRO LEU ASN PHE ARG ILE ASN SER ARG ASN LEU SER
SEQRES 23 A 334 ASP ILE GLY THR ILE MET ARG VAL VAL GLU LEU SER PRO
SEQRES 24 A 334 LEU LYS GLY SER VAL SER TRP THR GLY LYS PRO VAL SER
SEQRES 25 A 334 TYR TYR LEU HIS THR ILE ASP ARG THR ILE LEU GLU ASN
SEQRES 26 A 334 TYR PHE SER SER LEU LYS ASN PRO GLY
SEQRES 1 B 334 GLY PRO GLY GLU LYS LEU GLU LEU ARG LEU LYS SER PRO
SEQRES 2 B 334 VAL GLY ALA GLU PRO ALA VAL TYR PRO TRP PRO LEU PRO
SEQRES 3 B 334 VAL TYR ASP LYS HIS HIS ASP ALA ALA HIS GLU ILE ILE
SEQRES 4 B 334 GLU THR ILE ARG TRP VAL CYS GLU GLU ILE PRO ASP LEU
SEQRES 5 B 334 LYS LEU ALA MET GLU ASN TYR VAL LEU ILE ASP TYR ASP
SEQRES 6 B 334 THR LYS SER PHE GLU SER MET GLN ARG LEU CYS ASP LYS
SEQRES 7 B 334 TYR ASN ARG ALA ILE ASP SER ILE HIS GLN LEU TRP LYS
SEQRES 8 B 334 GLY THR THR GLN PRO MET LYS LEU ASN THR ARG PRO SER
SEQRES 9 B 334 THR GLY LEU LEU ARG HIS ILE LEU GLN GLN VAL TYR ASN
SEQRES 10 B 334 HIS SER VAL THR ASP PRO GLU LYS LEU ASN ASN TYR GLU
SEQRES 11 B 334 PRO PHE SER PRO GLU VAL TYR GLY GLU THR SER PHE ASP
SEQRES 12 B 334 LEU VAL ALA GLN MET ILE ASP GLU ILE LYS MET THR ASP
SEQRES 13 B 334 ASP ASP LEU PHE VAL ASP LEU GLY SER GLY VAL GLY GLN
SEQRES 14 B 334 VAL VAL LEU GLN VAL ALA ALA ALA THR ASN CYS LYS HIS
SEQRES 15 B 334 HIS TYR GLY VAL GLU LYS ALA ASP ILE PRO ALA LYS TYR
SEQRES 16 B 334 ALA GLU THR MET ASP ARG GLU PHE ARG LYS TRP MET LYS
SEQRES 17 B 334 TRP TYR GLY LYS LYS HIS ALA GLU TYR THR LEU GLU ARG
SEQRES 18 B 334 GLY ASP PHE LEU SER GLU GLU TRP ARG GLU ARG ILE ALA
SEQRES 19 B 334 ASN THR SER VAL ILE PHE VAL ASN ASN PHE ALA PHE GLY
SEQRES 20 B 334 PRO GLU VAL ASP HIS GLN LEU LYS GLU ARG PHE ALA ASN
SEQRES 21 B 334 MET LYS GLU GLY GLY ARG ILE VAL SER SER LYS PRO PHE
SEQRES 22 B 334 ALA PRO LEU ASN PHE ARG ILE ASN SER ARG ASN LEU SER
SEQRES 23 B 334 ASP ILE GLY THR ILE MET ARG VAL VAL GLU LEU SER PRO
SEQRES 24 B 334 LEU LYS GLY SER VAL SER TRP THR GLY LYS PRO VAL SER
SEQRES 25 B 334 TYR TYR LEU HIS THR ILE ASP ARG THR ILE LEU GLU ASN
SEQRES 26 B 334 TYR PHE SER SER LEU LYS ASN PRO GLY
HET 5EG A 401 29
HET K B1001 1
HET 5EG B1002 29
HETNAM 5EG 2-({5-[(2-CHLOROPHENOXY)METHYL]-1H-TETRAZOL-1-
HETNAM 2 5EG YL}ACETYL)-N-(4-CHLOROPHENYL)HYDRAZINECARBOXAMIDE
HETNAM K POTASSIUM ION
FORMUL 3 5EG 2(C17 H15 CL2 N7 O3)
FORMUL 4 K K 1+
FORMUL 6 HOH *177(H2 O)
HELIX 1 AA1 ALA A 33 ILE A 48 1 16
HELIX 2 AA2 ILE A 48 MET A 55 1 8
HELIX 3 AA3 SER A 67 GLY A 91 1 25
HELIX 4 AA4 SER A 103 VAL A 119 1 17
HELIX 5 AA5 ASP A 121 LEU A 125 5 5
HELIX 6 AA6 SER A 132 GLU A 138 5 7
HELIX 7 AA7 THR A 139 ILE A 151 1 13
HELIX 8 AA8 GLY A 167 THR A 177 1 11
HELIX 9 AA9 ALA A 188 GLY A 210 1 23
HELIX 10 AB1 SER A 225 ASN A 234 1 10
HELIX 11 AB2 GLY A 246 ALA A 258 1 13
HELIX 12 AB3 ASP A 286 THR A 289 5 4
HELIX 13 AB4 ARG A 319 ASN A 331 1 13
HELIX 14 AB5 ALA B 33 ILE B 48 1 16
HELIX 15 AB6 ILE B 48 MET B 55 1 8
HELIX 16 AB7 GLU B 56 ILE B 61 5 6
HELIX 17 AB8 SER B 67 GLY B 91 1 25
HELIX 18 AB9 SER B 103 VAL B 119 1 17
HELIX 19 AC1 ASP B 121 LEU B 125 5 5
HELIX 20 AC2 SER B 132 TYR B 136 5 5
HELIX 21 AC3 THR B 139 ILE B 151 1 13
HELIX 22 AC4 GLY B 167 THR B 177 1 11
HELIX 23 AC5 ALA B 188 GLY B 210 1 23
HELIX 24 AC6 SER B 225 ASN B 234 1 10
HELIX 25 AC7 GLY B 246 ALA B 258 1 13
HELIX 26 AC8 ASP B 286 THR B 289 5 4
HELIX 27 AC9 ARG B 319 ASN B 331 1 13
SHEET 1 AA1 2 GLU A 6 LEU A 9 0
SHEET 2 AA1 2 ALA A 18 PRO A 21 -1 O TYR A 20 N LEU A 7
SHEET 1 AA2 2 VAL A 26 ASP A 28 0
SHEET 2 AA2 2 HIS A 31 ASP A 32 -1 O HIS A 31 N ASP A 28
SHEET 1 AA3 7 TYR A 216 ARG A 220 0
SHEET 2 AA3 7 HIS A 181 GLU A 186 1 N GLY A 184 O GLU A 219
SHEET 3 AA3 7 LEU A 158 LEU A 162 1 N PHE A 159 O TYR A 183
SHEET 4 AA3 7 VAL A 237 VAL A 240 1 O PHE A 239 N VAL A 160
SHEET 5 AA3 7 ARG A 265 SER A 268 1 O ARG A 265 N ILE A 238
SHEET 6 AA3 7 TYR A 312 ILE A 317 -1 O HIS A 315 N ILE A 266
SHEET 7 AA3 7 MET A 291 LEU A 296 -1 N LEU A 296 O TYR A 312
SHEET 1 AA4 2 GLU B 6 LEU B 9 0
SHEET 2 AA4 2 ALA B 18 PRO B 21 -1 O TYR B 20 N LEU B 7
SHEET 1 AA5 2 VAL B 26 ASP B 28 0
SHEET 2 AA5 2 HIS B 31 ASP B 32 -1 O HIS B 31 N TYR B 27
SHEET 1 AA6 7 TYR B 216 ARG B 220 0
SHEET 2 AA6 7 HIS B 181 GLU B 186 1 N GLY B 184 O GLU B 219
SHEET 3 AA6 7 LEU B 158 LEU B 162 1 N PHE B 159 O TYR B 183
SHEET 4 AA6 7 VAL B 237 VAL B 240 1 O PHE B 239 N VAL B 160
SHEET 5 AA6 7 ARG B 265 SER B 268 1 O ARG B 265 N ILE B 238
SHEET 6 AA6 7 TYR B 312 ILE B 317 -1 O HIS B 315 N ILE B 266
SHEET 7 AA6 7 MET B 291 LEU B 296 -1 N LEU B 296 O TYR B 312
LINK O LYS B 52 K K B1001 1555 1555 2.66
LINK O LEU B 53 K K B1001 1555 1555 3.31
LINK O MET B 55 K K B1001 1555 1555 2.63
LINK OD1 ASN B 57 K K B1001 1555 1555 2.77
CISPEP 1 TRP A 22 PRO A 23 0 1.45
CISPEP 2 TRP B 22 PRO B 23 0 1.33
SITE 1 AC1 15 PHE A 131 PRO A 133 SER A 140 ASP A 161
SITE 2 AC1 15 GLY A 163 SER A 164 GLY A 165 VAL A 166
SITE 3 AC1 15 GLN A 168 VAL A 169 VAL A 240 ASN A 241
SITE 4 AC1 15 VAL A 267 SER A 268 SER A 269
SITE 1 AC2 4 LYS B 52 LEU B 53 MET B 55 ASN B 57
SITE 1 AC3 17 PHE B 131 PRO B 133 TYR B 136 SER B 140
SITE 2 AC3 17 ASP B 161 GLY B 163 SER B 164 GLY B 165
SITE 3 AC3 17 VAL B 166 GLN B 168 VAL B 169 PHE B 239
SITE 4 AC3 17 VAL B 240 ASN B 241 VAL B 267 SER B 268
SITE 5 AC3 17 SER B 269
CRYST1 158.712 158.712 73.645 90.00 90.00 120.00 P 63 12
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 0.006301 0.003638 0.000000 0.00000
SCALE2 0.000000 0.007275 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013579 0.00000